BiotiQuest® Gut Health & Probiotics Blog with Martha Carlin

How to Rebuild the Immune System After Antibiotics

Martha Carlin | Apr 11, 2024 | 10 minute read

Are you frequently falling ill or feeling run-down? It might be time for an immune system tune-up. Your immune system is your body's army, fighting off harmful invaders and keeping you healthy — but it might not always get the support it needs to keep you protected. 

In this blog post, we'll discuss different factors that form the backbone of your immune system: the gut microbiome and your diet. We’ll also look into how antibiotic treatments might alter your gut microbiome and share effective ways to support your immune system with diet and probiotics after a course of antibiotics. 

What makes for a healthy immune system?

Your gut houses 70-80% of the immune system and acts as the central hub of immune activity since it serves as the entry point and processing center for the majority of new stimuli (food, pathogens, and pollutants) that enter your body.

The mark of a healthy immune system is in its ability to have a balanced reaction — if it’s too weak, you might end up with frequent infections and bouts of sickness and if it’s too strong, you might end up with allergies and autoimmune disorders.

So, how does the immune system perform optimally and maintain a balanced state?

The innate and adaptive immune system

Your immune system functions at two levels: Innate immunity consists of general barrier immunity like the skin and mucosal barriers (gut mucosal wall) that act as the first line of defense against pathogens and protect you until the second level aka adaptive immunity can kick in. 

Mucosal immunity serves as one of the most effective defenses against pathogens. Over time, the gut mucus membrane traps pathogens and coats them in antibodies to make them ineffective and reduce the chance of infection. As the gut sheds the mucus as part of regular wear and tear, the trapped pathogens also get cleared off. But this might not always be the case if there’s a dysfunction in mucus-producing cells (goblet cells) or an imbalance in gut bacteria that support a healthy mucus wall.


Adaptive immunity consists of specialized cells such as T cells and B cells that might be slow to respond at first as they learn the pathogen but are highly effective in destroying its growth and preventing reinfection by creating memory immune cells.

On the flip side, if there’s a lack of tolerance in the immune system, even harmless triggers can lead to an exaggerated and often harmful immune response that might show up as autoimmune reactions or allergies.

Impact of gut microbiome on the development of the immune system

Mother-to-child transfer of gut bacteria helps in the development and maturation of a newborn’s gut microbiome as well as the development of gut immunity — GALTs (gut-associated lymphoid tissues) and the production of secretory immunoglobulin A (sIgA) from B cells. 

For instance, human milk oligosaccharides found in breast milk lead to the growth of B. infantis in the infant's gut. The metabolites produced by these bacterial species participate in the maturation of intestinal cells and have an anti-inflammatory effect.

Friend vs foe

A healthy gut microbiome imparts tolerance to the immune system. Without immune regulation, your immune system will mobilize against every nonself molecule including food and beneficial microbes even if they’re harmless, resulting in constant inflammation and harm to self tissue.

But, gut microbial metabolites (by-products) such as short chain fatty acids like butyrate and secondary bile acids exert a regulatory effect on immune cells and help develop immature immune cells into regulatory T cells that have an anti-inflammatory effect.


Does your gut health impact your immune system response?

Your gut microbiota composition plays a crucial role in establishing your immune responses as different microbial species impact the immune system differently. Your core gut microbiome establishes itself by the time you turn three years old and acts as an additional layer of protection against pathogens since it is highly resistant to change and colonization by new microbes (colonization resistance).

Despite colonization resistance, chronic conditions such as a diet high in processed foods and sugar, an unhealthy lifestyle, acute starvation, and exposure to antibiotics can lead to an unstable gut microbiome.

Not all microbes confer the same protective effects on the gut and the immune system. In a dysbiotic state (more pathogens than beneficial bacteria in the gut), an abundance of bacterial endotoxins such as Lipopolysaccharides (LPS) might lead to low-grade chronic inflammation due to a leaky gut.

The gut wall consists of a mucosal layer, a layer of epithelial cells, as well as various chemical protectants. The mucosal barrier makes sure that gut bacteria do not directly make contact with the epithelial layer and thus protects you from a pro-inflammatory immune response. 

The role of gut bacteria diversity in gut immunity

Under ideal conditions, different gut bacteria reside in harmony and have a give-and-take relationship. The human gut microbiota consists of Firmicutes and Bacteroidetes along with Proteobacteria and Actinobacteria. Changes in the abundances of different species can mean changes in the microbial metabolites and functional effects specific to certain species. 

For instance, a reduction in butyrate-producing bacteria due to a shift in your diet might lead to increased hunger, fat storage, and inflammation. Butyrate also supports an anaerobic environment in the gut which is essential for the maintenance of a diverse gut environment in addition to acting as a primary energy source for intestinal cells. A rise in oxygen due to a lack of butyrate will give opportunistic bacteria (that thrive in the presence of oxygen) a chance to proliferate and further disturb the integrity of the gut wall.

Butyrate-producing bacterial species also induce the development of regulatory T cells that have an anti-inflammatory immune response. On the other hand, Candidatus Savagella, also called segmented filamentous bacteria (SFB) are potent inducers of Th17 cells. Th17 cells are proinflammatory immune cells that protect you against infections. A decrease in SFB can lower your capacity to fight off pathogens due to reduced Th17 cells.

Your immune and digestive systems will have everything they need for optimum function as long as there is a balance between different bacterial species in the gut with the help of a varied diet that includes grass-fed protein sources and organic, naturally dried legumes (not dried by glyphosate); healthy fats from seeds and nuts such as sunflower seeds and almonds; complex carbohydrates and prebiotics from food sources such as onions, leeks, garlic, artichokes, etc.; fermented foods rich in probiotics such as kimchi and yogurt in addition to probiotics supplements rich in probiotic strains like lactobacillus and bifidobacteria genres such as L. plantarum and B. subtilis.

Additionally, recent probiotic and prebiotic studies suggest a carnivore diet might lend a hand in increasing microbiome diversity since hyaluronic acid, a structural part of body tissues, might act as a prebiotic source for gut bacteria.


How do antibiotics impact gut health?

Broad-spectrum antibiotics act on a wide range of gut bacteria with no distinction, clearing off a chunk of your microbiota (including beneficial bacteria) and leaving gaps in the community. This allows pathogenic bacteria such as C. difficile to grow in the absence of competition for space and resources. 

Antibiotic treatments might also lead to a dominance of antibiotic-resistant strains such as adherent invasive E. coli (AIEC) in the gut. Antibiotic-associated diarrhea (ADD) due to infections with C. difficile is a common occurrence after antibiotics. Additionally, antibiotic exposure has been associated with the development of Irritable Bowel Syndrome (IBS). 

Studies suggest an increase in mucolytic pathogenic bacteria such as proteobacteria like adherent invasive E. coli (AIEC) leads to gaps in the gut mucosal wall and that allows for an inflammatory immune reaction.

Some of the most commonly used antibiotic classes are β lactams including amoxicillin and ampicillin and glycopeptides such as vancomycin which inhibit bacterial growth by hindering bacterial cell wall synthesis. 

The introduction of antibiotics to the gut does not stop at inhibiting the growth of infectious bacteria but it also decreases the growth of beneficial bacteria such as bifidobacteria and lactobacillus and provides growth opportunities to antibiotic-resistant pathogenic bacteria such as AIEC. 

Studies also connect the use of antibiotics with an increase in gram-negative bacteria like proteobacteria resulting in higher serum LPS (lipopolysaccharide levels), which is associated with chronic inflammation and the development of several metabolic conditions.

How can you restore gut health and rebuild the immune system after antibiotics?

One of the best ways to restore your gut microbiota after a course of antibiotics is by being mindful of your diet, reintroducing beneficial bacteria to the gut via fermented foods, making lifestyle changes including exercise, and optimum sleep as well as introducing carefully formulated probiotic supplements such as those that have resulted from our BioFlux® model such as the Sugar Shift®.

Prebiotics, probiotic supplements, and exercise

Our diets impact the composition of our gut microbiome, especially when there’s a dramatic change due to the consumption of antibiotics. 

Foods that contain prebiotics such as soluble fiber, resistant starch, fructo-oligosaccharides, galacto-oligosaccharides, etc. such as garlic, onions, green banana, chicory (inulin), etc. and fermented foods rich in probiotics such as kimchi, homemade yogurt, and sauerkraut can support the growth of beneficial bacteria in the gut.

According to a systematic review and meta-analysis that evaluated 42 studies, co-administering probiotics with antibiotics reduces the risk of antibiotic-associated diarrhea by 37%. 

Additionally, according to a review article published in Oxidative Medicine and Cellular Longevity, moderate exercise might enhance the number of beneficial bacteria in the gut. Diet, probiotics, and exercise can be used together to accelerate the way to gut health recovery.

Abundances of beneficial bacteria like bifidobacteria and lactobacillus that generally take a hit during and after an antibiotic treatment might benefit from adding probiotic supplements like Ideal Immunity® and Antibiotic Antidote®.

Front view of glass bottle with 30 capsules of Antibiotic Antidote .Not all probiotic supplements perform the same, our probiotic formulations have resulted from our BioFlux® model studying complex data sets to predict microbial interactions, how they work, what they produce, impact each other, and your gut.

Antibiotic Antidote® was specifically developed to create the right environment to enable friendly bacteria to flourish again after taking antibiotics. As your body rebuilds its ecosystem, it targets free radicals generated by antibiotic use, strengthens the mucosal lining, and balances pH in the gut.

Ideal Immunity® targets the way your gut microbiome interacts with your immune system. It helps fortify mucosal surfaces, fights off pathogens, reduces toxic load, and gives your body a boost so you can feel good.  

Restoring your gut after antibiotics

We are constantly being challenged by pathogens and environmental toxins that tax the body and impact our immune system. Strengthening the lining of the gut provides the critical immune barrier to keep you healthy. Antibiotics destroy or slow down bacterial growth and leave the immune system compromised. While gut restoration can take several months to re-establish itself, probiotics are an easy way to help support your immune system and your journey to better health.

Frequently Asked Questions:

1. How do you restore your system after antibiotics?

Foods high in probiotics such as soluble fiber, oligosaccharides like garlic and green bananas, fermented foods such as kimchi and yogurt, and probiotic supplements such as Antibiotic Antidote® might help you restore your digestive system.

2. How do I get my gut bacteria back to normal?

As you recover, prebiotic and probiotic-rich foods such as garlic and kimchi along with probiotics such as Ideal Immunity® might help your gut bacteria get back to normal.

3. How long does it take for gut bacteria to recover after antibiotics?

It can take up to a couple of months for you to recover from a course of antibiotics. You can aid your gut recovery by adding gentle exercise and a range of prebiotic and probiotic foods and supplements to your diet.

4. What probiotics are best to restore the gut after antibiotics? 

Antibiotic treatments generally lower bifidobacterium and lactobacillus genera in your gut while increasing inflammatory species such as gram-negative proteobacteria like adherent invasive E. coli (AIEC). Probiotics such as Ideal Immunity® and Antibiotic Antidote® are great ways to reintroduce beneficial bacteria to your gut.

5. How do you reset your digestive system?

Fermented foods and foods rich in prebiotics are a great way to reset your digestive system. But be mindful as you add new foods to your diet, take it slow, and listen to your gut.

With gratitude,

Martha Carlin photo Martha Carlin, is a “Citizen Scientist”, systems thinker, wife of Parkinson’s warrior, John Carlin, and founder of The BioCollective , a microbiome company expanding the reach of science and BiotiQuest, the first of it’s kind probiotic line. Since John’s diagnosis in 2002, Martha began learning the science of agriculture, nutrition, environment, infectious disease, Parkinson’s pathology and much more. In 2014, when the first research was published showing a connection between the gut bacteria and the two phenotypes of Parkinson’s, Martha quit her former career as a business turnaround expert and founded The BioCollective to accelerate the discovery of the impact of gut health on all human disease. Martha was a speaker at the White House 2016 Microbiome Initiative launch, challenging the scientific community to “think in a broader context”. Her systems thinking background and experience has led to collaborations across the scientific spectrum from neuroscience to engineering to infectious disease. She is a respected out of the box problem solver in the microbiome field and brings a unique perspective to helping others understand the connections from the soil to the food to our guts and our brains.

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